[gmx-users] POPC simulation

Marc F. Lensink lensink at scmbb.ulb.ac.be
Thu Nov 1 13:47:40 CET 2007

On Thu, Nov 01, 2007 at 12:36:33PM +0000, Moutusi Manna wrote:
> Hi
>   I want to perform   peptide + popc membrane simulation. I download popc128a.pdb from
>   (http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies).
>   Before I introduce the peptide into the membrane, the water layer had to be broadened to ensure full solvation of the peptide .I increase the water layer using the following commands
>   1. editconf  -f  popc128a.pdb  -o  po_box.pdb  -box  6.1065  6.1059  9.0000  -c
>   2. genbox  -cp  po_box.pdb  -cs  -o  po_sol.pdb  -p  lip.top
>   Now, the no. of water molecules over the bilayer  increased . But, the problem is that  there are water molecules inside the bilayer, which were absent incase of popc128a.pdb. How can I remove these offending water molecules?

calculate the average z position of the phosphorus atoms of both
layers, then remove all water molecules - of the just added set! -
that lie in between.


Marc F. Lensink
Centre for Structural Biology and Bioinformatics         SCMBB
Université Libre de Bruxelles          lensink at scmbb.ulb.ac.be
Boulevard du Triomphe - CP 263, B-1050 Brussels, Belgium
tel: +32 2 650 5411  secr: +32 2 650 2013  fax: +32 2 650 5425

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